Open Research in TopoStats
Laura Wiggins, Sylvia Whittle
What is TopoStats?
- Automated software for processing Atomic Force Microscopy images.
- Takes in data, produces pretty pictures and useful stats.
- Used for research into DNA, cancer and pharmaceuticals.
How we approach Open Research in TopoStats
FAIR4RS
TopoStats development has been guided by the FAIR4RS (FAIR 4 Research Software) principles.
- Findable
- Accessible
- Interoperable
- Reusable
Ease of installation
- TopoStats is installable through PIP:
- Pre-release versions are installable via GitHub:
git clone https://github.com/AFM-SPM/TopoStats.git
cd TopoStats
pip install -e .
Open project management
- Issues
- Project feature board
- Discussion Forums
- Milestones
- Code of Conduct
- Bug & Feature templates
Docs, Versioning & Ease of use
- Versioned releases
- Automatic publishing to ORDA
- Automatic API documentation
- Easy to use config files
- Jupyter Notebooks
- Running courses & workshops
Development workflow
- Python PEP-8
- Auto-formatting with Black
- Linting via Pylint & Flake8
- Pre-commit to ensure adherence
- Pre-commit CI on GitHub
- Comprehensive testing
- Constant refactoring & organisation
Acknowledgements
- Tom Catley
- Jean Du
- Tobi Firth
- Max Gamill
- Libby Holmes
- Rob Moorehead
- Alice Pyne
- Eddie Rollins
- Neil Shephard
- Billie Ward
- Laura Wiggins
- Sylvia Whittle